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Fine mapping and candidate gene analysis of qGSN5, a novel quantitative trait locus coordinating grain size and grain number in rice

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qGSN5, a novel quantitative trait locus coordinating grain size and grain number in rice, was fine-mapped to an 85.60-kb region. GS3 may be a suppressor of qGSN5.

Abstract

Grain size and grain number are two factors that directly determine rice grain yield; however, the underlying genetic mechanisms are complicated and remain largely unclear. In this study, a chromosome segment substitution line (CSSL), CSSL28, which showed increased grain size and decreased grain number per panicle, was identified in a set of CSSLs derived from a cross between 93-11 (recipient) and Nipponbare (donor). Four substitution segments were identified in CSSL28, and the substitution segment located on chromosome 5 was responsible for the phenotypes of CSSL28. Thus, we defined this quantitative trait locus (QTL) as grain size and grain number 5 (qGSN5). Cytological and quantitative PCR analysis showed that qGSN5 regulates the development of the spikelet hull by affecting cell proliferation. Genetic analysis showed that qGSN5 is a semi-dominant locus regulating grain size and grain number. Through map-based cloning and overlapping substitution segment analysis, qGSN5 was finally delimited to an 85.60-kb region. Based on sequence and quantitative PCR analysis, Os05g47510, which encodes a P-type pentatricopeptide repeat protein, is the most likely candidate gene for qGSN5. Pyramiding analysis showed that the effect of qGSN5 was significantly lower in the presence of a functional GS3 gene, indicating that GS3 may be a suppressor of qGSN5. In addition, we found that qGSN5 could improve the grain shape of hybrid rice. Together, our results lay the foundation for cloning a novel QTL coordinating grain size and grain number in rice and provide a good genetic material for long-grain hybrid rice breeding.

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Acknowledgements

This work was supported by grants from the Major Research program of the National Natural Science Foundation of China (92535301), the National Natural Science Foundation of China (32001489), the Open project of Sichuan Provincial Key Laboratory of Crop Resources and Genetic Improvement, and the Outstanding Young Scientific and Technological Talents Project in Sichuan Province (2020JDJQ0040).

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  1. Hua Yuan, Peng Gao and Xiaoling Hu have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China

    Hua Yuan, Min Yuan, Xiaobo Zhu, Ting Li & Shigui Li

  2. Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Peng Gao, Xiaoling Hu, Zhengyan Xu, Mengya Jin, Wencheng Song, Shijie Zhan, Bin Tu, Yuping Wang, Bingtian Ma, Peng Qin, Weilan Chen & Shigui Li

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  1. Hua Yuan
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  2. Peng Gao
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  3. Xiaoling Hu
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  4. Min Yuan
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Contributions

HY and SL conceived and designed all the experiments. HY, PG, and XH performed most of the experiments and contributed equally to this work. MY, ZX, MJ, WS, and SZ participated in construction of plant materials, agronomic trait investigation, and primary mapping. XZ, BT, TL, and YW performed cytological analysis and fine mapping. BM, PQ, and WC were involved in candidate gene analysis and exploration of breeding utilization. HY wrote the manuscript, and all authors approved the final manuscript.

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Correspondence to Weilan Chen or Shigui Li.

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Communicated by Jiankang Wang.

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Yuan, H., Gao, P., Hu, X. et al. Fine mapping and candidate gene analysis of qGSN5, a novel quantitative trait locus coordinating grain size and grain number in rice. Theor Appl Genet 135, 51–64 (2022). https://doi.org/10.1007/s00122-021-03951-7

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